# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 23:35:26 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]-5-{[2-(pyridin-2-yl)ethyl]amino}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cc(NCCc3ccccn3)cc(c2)C#N)c1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 SK6  SK6  3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]-5-{[2-(pyridin-2-yl)ethyl]amino}benzonitrile  ligand  50  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SK6
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 SK6  N01   N  N     0  -0.487  -5.4557  -0.4985   0.0153
 SK6  C02   C  CR6   0   0.439  -6.7245  -0.1995   0.2676
 SK6  C03   C  CR16  0  -0.448  -7.2292   1.1069   0.1373
 SK6  C04   C  CR6   0   0.206  -6.3792   2.1172  -0.2605
 SK6  C05   C  CR16  0  -0.434  -5.0422   1.7895  -0.5196
 SK6  C06   C  CR6   0   0.284  -4.6315   0.4779  -0.3715
 SK6  N07   N  NH2   0  -0.838  -7.5486  -1.2303   0.6198
 SK6  C08   C  CH3   0  -0.726  -6.8575   3.5284  -0.4122
 SK6  C09   C  CH2   0  -0.490  -3.2070   0.0773  -0.6341
 SK6  C10   C  CH2   0  -0.515  -2.5291  -0.5156   0.6076
 SK6  C11   C  CR6   0   0.157  -1.1075  -0.9055   0.3170
 SK6  C12   C  CR16  0  -0.388  -0.0908   0.0263   0.4409
 SK6  C13   C  CR6   0   0.421   1.2459  -0.2742   0.1277
 SK6  C14   C  CR16  0  -0.375   1.5449  -1.5674  -0.3118
 SK6  C15   C  CR6   0   0.052   0.5154  -2.4984  -0.4365
 SK6  C16   C  CR16  0  -0.357  -0.8053  -2.1897  -0.1313
 SK6  N17   N  NH1   0  -0.702   2.2013   0.6964   0.2337
 SK6  C18   C  CH2   0  -0.260   3.6114   0.4037   0.1439
 SK6  C19   C  CH2   0  -0.531   4.4248   1.6834   0.3102
 SK6  C20   C  CR6   0   0.247   5.8958   1.3982   0.2181
 SK6  N21   N  N     0  -0.418   6.4852   0.9100   1.3078
 SK6  C22   C  CR16  0  -0.081   7.7786   0.6163   1.2526
 SK6  C23   C  CR16  0  -0.328   8.5558   0.7899   0.1173
 SK6  C24   C  CR16  0  -0.150   7.9439   1.2965  -1.0191
 SK6  C25   C  CR16  0  -0.342   6.5937   1.6047  -0.9686
 SK6  C26   C  CSP   0   0.045   0.8341  -3.8182  -0.8823
 SK6  N27   N  NS    0  -0.257   1.0882  -4.8834  -1.2413
 SK6  H03   H  HCR6  0   0.255  -8.2721   1.3079   0.3512
 SK6  H05   H  HCR6  0   0.243  -4.3372   2.5507  -0.8300
 SK6  HN07  H  HNH2  0   0.379  -7.0932  -2.0600   0.9636
 SK6  HN0A  H  HNH2  0   0.388  -8.3959  -0.9980   1.1108
 SK6  H08   H  HCH3  0   0.252  -6.3253   4.1934   0.2697
 SK6  H08A  H  HCH3  0   0.251  -6.6714   3.8938  -1.4231
 SK6  H08B  H  HCH3  0   0.247  -7.9231   3.6203  -0.2091
 SK6  H09   H  HCH2  0   0.251  -3.1845  -0.6632  -1.4394
 SK6  H09A  H  HCH2  0   0.250  -2.6388   0.9422  -0.9832
 SK6  H10   H  HCH2  0   0.253  -2.5548   0.2158   1.4187
 SK6  H10A  H  HCH2  0   0.254  -3.0966  -1.3852   0.9427
 SK6  H12   H  HCR6  0   0.261  -0.3326   1.0253   0.7888
 SK6  H14   H  HCR6  0   0.287   2.5574  -1.8591  -0.5521
 SK6  H16   H  HCR6  0   0.264  -1.5780  -2.9394  -0.2339
 SK6  HN17  H  HNH1  0   0.387   1.9555   1.4801   0.8181
 SK6  H18   H  HCH2  0   0.230   3.9259  -0.3304   0.8974
 SK6  H18A  H  HCH2  0   0.239   3.8314  -0.0321  -0.8349
 SK6  H19   H  HCH2  0   0.258   4.1311   2.4024  -0.4571
 SK6  H19A  H  HCH2  0   0.258   4.2054   2.1288   1.2840
 SK6  H22   H  HCR6  0   0.261   8.2222   0.2244   2.1614
 SK6  H23   H  HCR6  0   0.269   9.6069   0.5372   0.1288
 SK6  H24   H  HCR6  0   0.273   8.5086   1.4517  -1.9292
 SK6  H25   H  HCR6  0   0.266   6.0843   2.0034  -1.8361

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 SK6  N01  C02   aromatic  1.328  0.020  1.328
 SK6  N01  C06   aromatic  1.335  0.020  1.335
 SK6  C02  C03   aromatic  1.407  0.020  1.407
 SK6  C02  N07   single    1.366  0.020  1.366
 SK6  C03  C04   aromatic  1.379  0.020  1.379
 SK6  C04  C05   aromatic  1.401  0.020  1.401
 SK6  C04  C08   single    1.498  0.020  1.498
 SK6  C05  C06   aromatic  1.382  0.020  1.382
 SK6  C06  C09   single    1.503  0.020  1.503
 SK6  C09  C10   single    1.534  0.020  1.534
 SK6  C10  C11   single    1.502  0.020  1.502
 SK6  C11  C12   aromatic  1.385  0.020  1.385
 SK6  C11  C16   aromatic  1.393  0.020  1.393
 SK6  C12  C13   aromatic  1.405  0.020  1.405
 SK6  C13  C14   aromatic  1.398  0.020  1.398
 SK6  C13  N17   single    1.366  0.020  1.366
 SK6  C14  C15   aromatic  1.394  0.020  1.394
 SK6  C15  C16   aromatic  1.390  0.020  1.390
 SK6  C15  C26   single    1.429  0.020  1.429
 SK6  N17  C18   single    1.443  0.020  1.443
 SK6  C18  C19   single    1.525  0.020  1.525
 SK6  C19  C20   single    1.501  0.020  1.501
 SK6  C20  N21   aromatic  1.332  0.020  1.332
 SK6  C20  C25   aromatic  1.392  0.020  1.392
 SK6  N21  C22   aromatic  1.327  0.020  1.327
 SK6  C22  C23   aromatic  1.387  0.020  1.387
 SK6  C23  C24   aromatic  1.387  0.020  1.387
 SK6  C24  C25   aromatic  1.386  0.020  1.386
 SK6  C26  N27   triple    1.152  0.020  1.152
 SK6  C03  H03   single    0.930  0.020  1.080
 SK6  C05  H05   single    0.930  0.020  1.080
 SK6  N07  HN07  single    0.890  0.020  1.040
 SK6  N07  HN0A  single    0.890  0.020  1.040
 SK6  C08  H08   single    0.970  0.020  1.090
 SK6  C08  H08A  single    0.970  0.020  1.090
 SK6  C08  H08B  single    0.970  0.020  1.090
 SK6  C09  H09   single    0.970  0.020  1.090
 SK6  C09  H09A  single    0.970  0.020  1.090
 SK6  C10  H10   single    0.970  0.020  1.090
 SK6  C10  H10A  single    0.970  0.020  1.090
 SK6  C12  H12   single    0.930  0.020  1.080
 SK6  C14  H14   single    0.930  0.020  1.080
 SK6  C16  H16   single    0.930  0.020  1.080
 SK6  N17  HN17  single    0.890  0.020  1.040
 SK6  C18  H18   single    0.970  0.020  1.090
 SK6  C18  H18A  single    0.970  0.020  1.090
 SK6  C19  H19   single    0.970  0.020  1.090
 SK6  C19  H19A  single    0.970  0.020  1.090
 SK6  C22  H22   single    0.930  0.020  1.080
 SK6  C23  H23   single    0.930  0.020  1.080
 SK6  C24  H24   single    0.930  0.020  1.080
 SK6  C25  H25   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 SK6  C06   N01  C02   118.70  3.000
 SK6  N07   C02  C03   120.55  3.000
 SK6  N07   C02  N01   117.10  3.000
 SK6  C03   C02  N01   122.31  3.000
 SK6  H03   C03  C04   120.96  3.000
 SK6  H03   C03  C02   119.97  3.000
 SK6  C04   C03  C02   119.08  3.000
 SK6  C08   C04  C05   120.43  3.000
 SK6  C08   C04  C03   121.51  3.000
 SK6  C05   C04  C03   118.06  3.000
 SK6  H05   C05  C06   120.28  3.000
 SK6  H05   C05  C04   120.66  3.000
 SK6  C06   C05  C04   119.06  3.000
 SK6  C09   C06  C05   121.05  3.000
 SK6  C09   C06  N01   116.15  3.000
 SK6  C05   C06  N01   122.80  3.000
 SK6  HN0A  N07  HN07  113.85  3.000
 SK6  HN0A  N07  C02   117.35  3.000
 SK6  HN07  N07  C02   115.91  3.000
 SK6  H08B  C08  H08A  108.15  3.000
 SK6  H08B  C08  H08   108.02  3.000
 SK6  H08A  C08  H08   106.96  3.000
 SK6  H08B  C08  C04   111.91  3.000
 SK6  H08A  C08  C04   110.79  3.000
 SK6  H08   C08  C04   110.81  3.000
 SK6  H09A  C09  H09   106.85  3.000
 SK6  H09A  C09  C10   109.57  3.000
 SK6  H09   C09  C10   108.97  3.000
 SK6  H09A  C09  C06   109.75  3.000
 SK6  H09   C09  C06   109.17  3.000
 SK6  C10   C09  C06   112.36  3.000
 SK6  H10A  C10  H10   107.05  3.000
 SK6  H10A  C10  C11   110.17  3.000
 SK6  H10   C10  C11   109.86  3.000
 SK6  H10A  C10  C09   109.07  3.000
 SK6  H10   C10  C09   109.38  3.000
 SK6  C11   C10  C09   111.22  3.000
 SK6  C16   C11  C12   119.33  3.000
 SK6  C16   C11  C10   120.44  3.000
 SK6  C12   C11  C10   120.18  3.000
 SK6  H12   C12  C13   118.70  3.000
 SK6  H12   C12  C11   118.99  3.000
 SK6  C13   C12  C11   122.31  3.000
 SK6  N17   C13  C14   122.14  3.000
 SK6  N17   C13  C12   119.74  3.000
 SK6  C14   C13  C12   118.11  3.000
 SK6  H14   C14  C15   119.46  3.000
 SK6  H14   C14  C13   121.33  3.000
 SK6  C15   C14  C13   119.21  3.000
 SK6  C26   C15  C16   119.04  3.000
 SK6  C26   C15  C14   118.69  3.000
 SK6  C16   C15  C14   122.27  3.000
 SK6  H16   C16  C15   120.27  3.000
 SK6  H16   C16  C11   120.96  3.000
 SK6  C15   C16  C11   118.77  3.000
 SK6  HN17  N17  C18   115.60  3.000
 SK6  HN17  N17  C13   115.27  3.000
 SK6  C18   N17  C13   122.31  3.000
 SK6  H18A  C18  H18   106.86  3.000
 SK6  H18A  C18  C19   108.94  3.000
 SK6  H18   C18  C19   109.47  3.000
 SK6  H18A  C18  N17   109.46  3.000
 SK6  H18   C18  N17   111.90  3.000
 SK6  C19   C18  N17   110.13  3.000
 SK6  H19A  C19  H19   107.69  3.000
 SK6  H19A  C19  C20   109.19  3.000
 SK6  H19   C19  C20   110.22  3.000
 SK6  H19A  C19  C18   109.39  3.000
 SK6  H19   C19  C18   109.41  3.000
 SK6  C20   C19  C18   110.88  3.000
 SK6  C25   C20  N21   122.01  3.000
 SK6  C25   C20  C19   121.03  3.000
 SK6  N21   C20  C19   116.94  3.000
 SK6  C22   N21  C20   118.58  3.000
 SK6  H22   C22  C23   120.13  3.000
 SK6  H22   C22  N21   116.34  3.000
 SK6  C23   C22  N21   123.53  3.000
 SK6  H23   C23  C24   121.54  3.000
 SK6  H23   C23  C22   120.46  3.000
 SK6  C24   C23  C22   117.99  3.000
 SK6  H24   C24  C25   120.47  3.000
 SK6  H24   C24  C23   120.75  3.000
 SK6  C25   C24  C23   118.77  3.000
 SK6  H25   C25  C24   120.75  3.000
 SK6  H25   C25  C20   120.13  3.000
 SK6  C24   C25  C20   119.12  3.000
 SK6  N27   C26  C15   180.00  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 SK6  CONST_01  C04  C03  C02  N01     0.00   0.0  0
 SK6  CONST_02  C04  C05  C06  N01     0.00   0.0  0
 SK6  CONST_03  C05  C06  N01  C02     0.00   0.0  0
 SK6  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 SK6  CONST_05  C06  N01  C02  C03     0.00   0.0  0
 SK6  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 SK6  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 SK6  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 SK6  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 SK6  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 SK6  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 SK6  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 SK6  CONST_13  C23  C22  N21  C20     0.00   0.0  0
 SK6  CONST_14  C23  C24  C25  C20     0.00   0.0  0
 SK6  CONST_15  C24  C25  C20  N21     0.00   0.0  0
 SK6  CONST_16  C24  C23  C22  N21     0.00   0.0  0
 SK6  CONST_17  C25  C20  N21  C22     0.00   0.0  0
 SK6  CONST_18  C25  C24  C23  C22     0.00   0.0  0
 SK6  CONST_19  C09  C06  N01  C02   180.00   0.0  0
 SK6  CONST_20  C08  C04  C03  C02   180.00   0.0  0
 SK6  CONST_21  N07  C02  C03  C04   180.00   0.0  0
 SK6  CONST_22  C09  C06  C05  C04   180.00   0.0  0
 SK6  CONST_23  N07  C02  N01  C06   180.00   0.0  0
 SK6  CONST_24  C08  C04  C05  C06   180.00   0.0  0
 SK6  CONST_25  C13  C12  C11  C10   180.00   0.0  0
 SK6  CONST_26  C15  C16  C11  C10   180.00   0.0  0
 SK6  CONST_27  N17  C13  C12  C11   180.00   0.0  0
 SK6  CONST_28  C26  C15  C16  C11   180.00   0.0  0
 SK6  CONST_29  C26  C15  C14  C13   180.00   0.0  0
 SK6  CONST_30  N17  C13  C14  C15   180.00   0.0  0
 SK6  CONST_31  C22  N21  C20  C19   180.00   0.0  0
 SK6  CONST_32  C24  C25  C20  C19   180.00   0.0  0
 SK6  CONST_33  H03  C03  C02  N01   180.00   0.0  0
 SK6  CONST_34  H05  C05  C06  N01   180.00   0.0  0
 SK6  CONST_35  H16  C16  C11  C12   180.00   0.0  0
 SK6  CONST_36  H14  C14  C13  C12   180.00   0.0  0
 SK6  CONST_37  H12  C12  C13  C14   180.00   0.0  0
 SK6  CONST_38  H22  C22  N21  C20   180.00   0.0  0
 SK6  CONST_39  H24  C24  C25  C20   180.00   0.0  0
 SK6  CONST_40  H25  C25  C20  N21   180.00   0.0  0
 SK6  CONST_41  H23  C23  C22  N21   180.00   0.0  0
 SK6  CONST_42  C18  N17  C13  C12   180.00   0.0  0
 SK6  CONST_43  C18  N17  C13  C14     0.00   0.0  0
 SK6  Var_01    C10  C09  C06  N01   -60.23  30.0  2
 SK6  Var_02    C11  C10  C09  C06  -179.95  30.0  3
 SK6  Var_03    C12  C11  C10  C09    86.79  30.0  2
 SK6  Var_04    N21  C20  C19  C18   -80.06  30.0  2
 SK6  Var_05    H08  C08  C04  C03   118.58  30.0  2
 SK6  Var_06    C19  C18  N17  C13  -179.55  30.0  3
 SK6  Var_07    C20  C19  C18  N17  -179.94  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 SK6  plan-1  N01   0.020
 SK6  plan-1  C02   0.020
 SK6  plan-1  C03   0.020
 SK6  plan-1  C04   0.020
 SK6  plan-1  C05   0.020
 SK6  plan-1  C06   0.020
 SK6  plan-1  N07   0.020
 SK6  plan-1  C08   0.020
 SK6  plan-1  C09   0.020
 SK6  plan-1  H03   0.020
 SK6  plan-1  H05   0.020
 SK6  plan-2  C10   0.020
 SK6  plan-2  C11   0.020
 SK6  plan-2  C12   0.020
 SK6  plan-2  C13   0.020
 SK6  plan-2  C14   0.020
 SK6  plan-2  C15   0.020
 SK6  plan-2  C16   0.020
 SK6  plan-2  N17   0.020
 SK6  plan-2  C26   0.020
 SK6  plan-2  N27   0.020
 SK6  plan-2  H12   0.020
 SK6  plan-2  H14   0.020
 SK6  plan-2  H16   0.020
 SK6  plan-3  C19   0.020
 SK6  plan-3  C20   0.020
 SK6  plan-3  N21   0.020
 SK6  plan-3  C22   0.020
 SK6  plan-3  C23   0.020
 SK6  plan-3  C24   0.020
 SK6  plan-3  C25   0.020
 SK6  plan-3  H22   0.020
 SK6  plan-3  H23   0.020
 SK6  plan-3  H24   0.020
 SK6  plan-3  H25   0.020
 SK6  plan-4  C02   0.020
 SK6  plan-4  N07   0.020
 SK6  plan-4  HN07  0.020
 SK6  plan-4  HN0A  0.020
 SK6  plan-5  C13   0.020
 SK6  plan-5  N17   0.020
 SK6  plan-5  C18   0.020
 SK6  plan-5  HN17  0.020

